


From the Shadows

by ValkeryVale



Category: Sherlock (TV), Sherlock Holmes & Related Fandoms
Genre: Adventure, Angst, Can't tag everything without revealing surprises, Danger, F/M, M/M, Plot, Romance, Season/Series 3 Compliant, Slow Burn
Language: English
Status: In-Progress
Published: 2014-03-23
Updated: 2014-03-27
Packaged: 2018-01-16 17:04:02
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 4,214
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1355038
Author URL: https://archiveofourown.org/users/ValkeryVale/pseuds/ValkeryVale
Summary: <blockquote class="userstuff">
              <p>After the devastation Sherlock Holmes brought down on the network, Moran clung to the remnants. Just as Moran was rebuilding, a new enemy has appeared on the horizon. Solomon Rust. Ruthless, heartless, soulless bastard that was tearing his world apart piece by piece, leaving a wake of dead bodies behind. His men were dying. Moran could not lose this battle.</p><p>Even if it meant working with an enemy.</p><p>It was time for Moran to engage the services of the world's only consulting detective.</p><p>Note: Follows after Season 3 Episode 3. My version of what happens next.  Sherlock must work with Sebastian Moran against a new enemy Solomon Rust. Mary's past comes to haunt them all, and she risks all to save her family. John and Sherlock's friendship is strained as John disapproves of Sebastian Moran. In the end, this case changes everything about Sherlock and John's relationship.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> Work in progress. Hope to update once a week.

Moran took aim just above center of his target – back of the head of a man in the town square below. The muscles in his arms and shoulders found that familiar tension point to keep the weapon still. Slowly, Moran squeezed the trigger part way, to be at the ready. He inhaled evenly and gently, held his breath for a moment and then exhaled cautiously.

Moran envisioned a few seconds into the future. There would be a percussive crack. He'd draw the bolt back quickly if he needed another shot – he wouldn't – then the spent shell would eject back over his shoulder. He'd get a glimpse of red mist as his target dropped to the ground.

 _And all of this will be over and I'll have my life back,_ Moran thought to himself.

The sound of his phone vibrating on the building's ledge pierced the calm. Moran quickly glanced to the screen to see who it was, even though he felt he already knew. Through his scope he saw his target pull a phone from his pocket and hold it up to his ear. He turned around and stared right at Moran.

 _Damn_.

Moran considered his options. He slowly released the trigger and eased his grip off, one finger at a time. He reached over to his phone, and pressed the speaker button.

"I see you," Moriarty's taunting, playful voice came through the phone. Moran stared at Moriarty through the scope as Moriarty gave a little wave.

"I noticed," Moran replied. He quickly placed his hand back on the rifle, his finger on the trigger, at the ready again.

"Did you really think I'd be alone?"

"I did," Moran said just as a red light filled his scope, blinding him for a moment. Even though he had hastily thrown his plan into action, he believed he knew where Moriarty's assets would be. And he believed Moriarty when he had said he was going to the meeting alone.

"Guess I was wrong," Moran added quickly.

"On second thought...," Moriarty said as Moran heard a finger snap, and the red light vanished.

"Go ahead and shoot. I do love surprises," Moriarty mocked.

"You have nothing else to hang over me now," Moran said, pressed his face further into the scope and re-gripped the rifle. _I should have done this a long time ago_.

"Oh, I'm so very sorry about your mummy, I really am. But you can't blame me...God did that! Blame him!" Moriarty exclaimed in a sing song voice. "Tell me something. What were you planning to do after you kill me Sebastian?"

"Anything I want," Moran responded.

"After all the blood you have on your hands, I don't think so. You'll spend the rest of your life in prison without my protection. Or find yourself really, really dead," Moriarty mocked again, and gave a half smile.

"It may be worth it – to take a bastard like you out," Moran said, trying to sound confident. "I could also disappear. You taught me how to do that."

"A life on the run, really...is that what you want? Have the past few years really been that horrible? Did I ever ask you to do anything unpleasant? Kill someone innocent?" Moriarty asked. "No. I didn't. You have this moral code thing in your military mind. I know you. That's why I only sent you to kill the really, really naughty ones"

Moran thought back and hesitated to respond. Moriarty pounced.

"I'll make you a deal. You don't kill me, I won't kill you, and I'll let you in on everything. You can add a little moral compass to the criminal world and I get to keep a very valuable asset that I worked so hard to acquire," Moriarty said.

"I don't understand. I'm aiming a rifle at you and you want to promote me?" Moran responded, astonished.

"Right."

"For me to do what?" Moran questioned.

"To be my right hand man. My confidant. Like I said, I know you. Your word is golden. If you make a commitment to me, you will honor it. And you can be trusted," Moriarty said as he leaned over a little. "Trust is a very valuable and rare commodity in my business."

Moran could not believe what he was hearing from Moriarty. The bitter pill of all was that he was actually considering his offer. Life on the run from his enemies, from Moriarty and the authorities...would not be the life he wanted.

Moriarty pressed on, "I have always kept my word with you Sebastian. I know how important that is to you. If you agree, I make this vow to you. You will not die by my hand or my order. And I will mentor you. I need you."

Moriarty spoke very slowly, with a quiet intensity "But...I am losing my patience with this little game. You either say yes or give me a bullet in the brain."

Moriarty hung up and slipped the phone in his pocket. He squared his shoulders and stared straight at Moran with a smug smile on his face. Moran rested his head against his rifle, then slowly set it down and stood up, shoving his hands into his pockets. Moriarty gave a mock salute, and walked away. Moran watched him disappear into the crowd.

* * *

Moran rubbed a hand over his face as he shook away the memory of that day, years ago. That was the day he found out his mother was dead and the day he made a deal with the devil.

A cold wind fluttered through his hair and flapped at his coat collar as he stared down at his mother's grave stone.

He couldn't even bury his mother properly because of that mad man. The grave stone said 'Cecilia T Hopkins'. After all the work Moriarty had done to make Sebastian Moran disappear from the world, Moriarty couldn't risk Moran getting caught visiting Margret Moran's grave.

After the devastation that Sherlock Holmes had brought down on the network the last two years, Moran clung to the remnants. The mercenary work, weapons trafficking, and cybercrime had survived in part because Moran had kept it as far away from Moriarty as possible. He ran those groups with military and terrorist methods. Keeping each cell independent of each other and completely in the dark about the rest of the network. His men were loyal and well trained. Together they went underground and stayed off Sherlock Holmes' radar until it was time to start again.

Just as Moran was rebuilding, a new enemy has appeared on the horizon. Solomon Rust. Ruthless, heartless, soulless bastard that was tearing his world apart piece by piece, leaving a wake of dead bodies behind. His men were dying. Moran could not lose this battle.

He took a few steps back from his mother's grave and cradled the dozen lilies he had. He watched quietly as his men slowly dug out the old grave stone and replaced it with a new one, engraved with

_Margret S Moran  
Beloved Wife and Mother_

He knelt down and rested his hand on top of the grave stone while he placed the lilies. He had only seen his mother once before she died. He wasn't there for her at the end. He never forgave Moriarty for that. He had been forced to sacrifice so much and he would fight for what remained. He wasn't going to let Solomon Rust take that away.

Even if it meant working with an enemy.

Moran ran his fingers over his mother's name. It was time he came out of the shadows and fight. Moran stood and brushed the dirt from his knees. He pulled out his phone and sent a simple one word text

_Now_

As he walked away, Moran smiled to himself. Having a ghost of Moriarty broadcasted across England should keep Sherlock Holmes in London and in the game.

It was time for Moran to engage the services of the world's only consulting detective.

* * *


	2. Chapter 2

**Notes for the Chapter:**

> Getting a bit more shored up with where this is going...

A loud bang and shuffle pushed through the sound of the shower. As John rinsed his hair out, he heard a closet door slam and Mary shout out a string of creative curses. He shut off the water and reached for a towel. As he dried himself off, Mary flung the bathroom door open.

She appeared flustered and disheveled, a bit comical with her large pregnant belly.

"Have you seen my ski bag?" She urgently asked John.

John gave a quirk of the head and a half smile, "You don't ski."

"Yes, I know I don't ski. But have you seen my ski bag?"

John wrapped the towel around his waist and reached for the shaving cream on the sink.

"What does it look like?" he asked As he started to lather his face.

Mary regarded him as if he had grown a second head.

"It's a bag. Longish. You know, made to hold skis," she responded, words dripping with sarcasm.

John turned his half-lathered face and looked at his wife.

"Are there skis in it?" he asked as innocently as he could muster.

"No, of course there aren't skis in it. I don't ski!" Mary shouted in frustration.

John let silence fall over the bathroom as he stared, smiling at Mary. She narrowed her eyes at him before shouting,

"Oh shut up, you're no help," and stomped out of the bathroom.

John gave a little chuckle to himself. Funny to see Mary, a normally calm, collected, intelligent woman be a bit frazzled. Must be those pregnancy hormones.

John finished pulling himself together, dressing in a button shirt and denims. He reached into the bottom drawer of his dresser for his gun, only to find the drawer empty.

_Right, the government has my gun. Being a murder weapon and all._

John stood up and looked into the mirror above the dresser. He remembered when Sherlock had slid the gun out from his pocket at Magnusson's house, Appledore.  
It took too long for John to register Sherlock's movements and in an instant, the gun had gone off and Magnusson lay dead by Sherlock's hand.

Once again, Sherlock leapt into the void in protection of his friends. Without consideration for the consequences. John couldn't help feel guilty for putting Sherlock into a position where he thought committing murder was the only way out. At least this time, perhaps John will be able to help Sherlock.

He turned and walked through the house, finding Mary in the sitting room, wrestling with a large white bag.

She glanced up and smiled, "I found it!"

"So, what's in bag?" John asked as he took a half step towards her.

Mary kept zipping and unzipping compartments, peaking inside each one, then she quickly answered, "None of your business, since you wouldn't help me find it."

John just narrowed his eyes and said, "So, you'll tell me later then?"

She looked up and smiled, "Yes, of course."

Mary leaned forward and John stepped closer, giving her a quick kiss on the check as he rubbed her shoulder.

"See you later then," John said as he stepped away. Mary just nodded and turned her attention back to the bag.

John grabbed his black jacket off of the hook and opened the front door. The well suited man by the door silently fell in stride behind John. They walked towards the black sedan idling at the curb. The man opened the car door for John and then jumped into the passenger's seat.

As they pulled away from his house, John let his mind wander and imagine what the day would bring.

The sedan stopped in front of 221B Baker St. John slid out of the car, gazed over the street and then glanced up to the windows. He found Sherlock standing there, with his violin perched under his chin, looking down at John.

John gave a smile and a nod of his head to his friend.

He thought back to the many times he had stood in that very spot, looking up at Sherlock in the window. Coming home from surgery. Walking back from Tesco. Grabbing a bite from Speedy's. After a long walk, blowing off steam from their many arguments.

All those times, he always felt glad to be home. But 221B wasn't his home anymore and that thought made his smile fade away.

He shook his head and strode towards the front door. Upon opening it, his ears were assailed with a dark melody, the notes seemed so mournful. The sound of the violin echoed hauntingly through the stairwell as John climbed up.

John walked into the sitting room to find Mycroft perched in John's chair, scanning through his phone.

Without moving, Mycroft said politely, "Good morning Dr. Watson."

John simply nodded and looked over to Sherlock who still faced the window, standing behind his chair, playing his violin. Sherlock had yet to turn and acknowledge John's presence in the flat.

Sherlock wore his blue dressing gown over a white button shirt and dark trousers. John noticed that the bottom of the dressing gown seemed to be moving independently of Sherlock. John shifted his position so he could see behind the chair, and he found a pair of stiletto heels attached to a kneeling woman in a very tight skirt.

Anthea called out from behind the chair, "Hello Dr. Watson."

John said slowly, "Uh, Hello." And then gave a curious look towards Mycroft, who still hadn't raised his head up.

Anthea carefully stood up and straightened her skirt. She set the tools she had in her hand onto the table as she gave the back of Sherlock's head a hateful stare. She gave John a curt nod, and walked past Mycroft.

She mumbled under her breath, "You don't pay me enough to deal with him," and then quickly walked out, her heels clicked loudly on the stairs.

At that point, Mycroft raised his head and looked sadly after Anthea, then asked, "Was that really necessary Sherlock? She's only doing her job."

The violin screeched an awful wail as Sherlock whipped around and jumped into his chair, carelessly setting his violin on the floor.

John glanced from one brother to the other, shifted from one foot to the other, then asked, "So, what's going on then?"

"My brother is being his usual unpleasant self, making it difficult to do my job," Mycroft said with a hint of anger.

"And what was Anthea doing?"

Mycroft opened his mouth but Sherlock quickly shouted out, "Fashion John! Mycroft's decided to make me more fashionable with this lovely ankle bracelet."

Sherlock leaned back in his chair and pulled his left trouser leg up to reveal a tracking ankle bracelet.

Mycroft set his phone down and folded his hands in his lap.

"It's better than prison, Sherlock," Mycroft said as he leveled his gaze at his younger brother.

Sherlock leaned forward in his chair, his face red with anger.

"I am not a threat Mycroft!"

"Only to those that threaten your friends," Mycroft remarked.

"Exactly," Sherlock said with a sharp nod.

Mycroft tilted his chin down as he replied, "That does seem to happen quite frequently, it's a wonder that you haven't left a trail of dead bodies."

John snorted a laugh at that, especially since he was often the friend in danger. Mycroft and Sherlock silently turned their heads and stared at John.

Mycroft cleared his throat and turned his attention back to Sherlock.

"These are the terms, until this situation with Moriarty is resolved. You did commit murder, dear brother."

Sherlock gave a small glance to John then Mycroft as he folded his arms across his chest. He let his gaze fall onto the skull on the mantel.

The guilt that John felt brewed again, that Sherlock was a murderer because of him and Mary. John took a deep breath and looked at Mycroft.

"Right, so what did you need from me Mycroft?" John asked.

"How's Mary handling this John?" Mycroft asked.

John quirked his head at the odd question, then clasped his hands behind his back.

"Fine. She's a bit...agitated that the man who once tried to blow me up into a million pieces has come back from the dead. Aside from that, she seems fine," John said with a tight smile.

"She seemed rather shocked at Moriarty's reappearance," Mycroft said slowly.

The words had some meaning behind them, but John didn't want to think about what that meaning could be. Silence hung in the air as John bit his tongue.

"I'm sure you have been wondering what the government has planned for you," Mycroft said.

"I, uh, no...no I hadn't been wondering at all. Why would the government have plans for me?" John asked Mycroft, with a puzzled stare.

Sherlock leaned forward onto his elbows, folded his hands, and looked at John.

"Since I was to go on a suicide mission to Eastern Europe, I had parlayed away any punishment for your part of the crime. All part of my deal," Sherlock elongated the last word, lacing it with spite as he stared daggers into his older brother.

John looked away from Sherlock and asked Mycroft, "Wh-What was my part?"

Mycroft's expression relayed that this should be obvious to John, that it pained him to explain.

"Conspiracy to commit treason, theft of government property, and possession of an illegal firearm," Mycroft rattled off.

John quickly darted his tongue across his bottom lip and looked down to the floor.

_Right, those are the crimes I committed._

"I was able to negotiate on your behalf a much more agreeable sentence than you would have faced in court," Mycroft said smoothly.

John raised his head and looked to his friend. Sherlock's expression and a quick smile told him that this was for the best. John tilted his head to the side, his face asking Mycroft to continue.

"You and Sherlock are now assigned to me. We are to get to the bottom of this business with Moriarty. Determine if he's alive and if so, eliminate him. If not, find out who is behind that little stunt and how were they able to infiltrate our entire communications network," Mycroft explained.

"So, my punishment is to help Sherlock solve the mystery of Moriarty's reappearance?" John asked.

Mycroft nodded.

John smiled, "I would have done that anyways."

Sherlock gave a laugh and John smiled widely back at him.

Mycroft frowned and continued, "That may be, but your time...your entire life will be dedicated to this case. No more surgery, no quiet evening dinners with the wife, your life as you know it is over until this is solved."

John let Mycroft's words soak in. He took a short step towards Mycroft as he started to seethe with anger, he stammered, "An-and how will I take care of Mary? And the baby? You can't just commender me!"

"You will be fairly compensated for your lost wages and certainly will be allowed to see your wife periodically. I am sure that Mary would concur, having you out of prison is the preferred solution," Mycroft argued his point.

"Mycroft, you can't possible expect John to abandon Mary - " Sherlock exclaimed, but was quickly interrupted by Mycroft.

"That's exactly what I expect. This is the best deal I could broker. And there remains a great deal of uncertainty as to what will happen to you even after this case if completed."

Mycroft continued, his voice slightly softer, "And I believe that we all know, Mary Watson is more than capable of taking care of herself."

Mycroft let his face betray his thoughts. Yes, he knew about Mary Watson's past. And his words hung in the air as John and Sherlock came to the realization at the same time.

Sherlock steepled his hands under his chin and asked, "How long have you known, about Mary?"

Mycroft ignored his brother and said to John, "You should have read that flash drive when you had the chance John."

"How long Mycroft!" Sherlock shouted, and Mycroft snapped his head to his brother.

"Since the wedding. I warned you not to get too involved Sherlock."

John staggered back and sat down on the sofa. He rubbed his hands over his face and then looked up.

"I-I don't understand. Why would you have looked into Mary's past?" John asked.

"If you had read the flash drive, you would know why. As you may have guessed, she's played on both sides of law, enough to get my attention," Mycroft said quietly.

"And why haven't you brought her in, arrested her?" John asked, still quite confused.

"Well, she is married to my little brother's best friend, perhaps I thought it was the right thing to do, keep her under wraps," Mycroft said with a smug smile.

Sherlock snorted a laugh loudly, "Don't be absurd Mycroft. You aren't keeping her secret out of some sense of loyalty towards John and I. You think you may have a use for her someday, and that you could press her into doing you dirty work. Honestly, you're no better than Magnusson," Sherlock spat the words out.

"Surely you can't mean that you're going to use her now?" John said with a pained voice.

"Certainly not, even I have the decency not to use a pregnant woman," Mycroft scoffed.

John breathed a small sigh of relief, but turned pleading eyes to Mycroft.

"You can't pull her back into that life again. She worked very hard to disappear and start over...to leave that part of herself behind."

"Do you really think that's what she's done? You think she just stopped, because she fell in love with you? Are you confident that she has left that life behind?" Mycroft said with an incredulous look.

Sherlock's deep voice rumbled, "You think she's still working?"

"I have no proof," Mycroft turned from his brother back to address John. "But you, Dr. Watson, know better than I how hard it is to leave that kind of life behind. To leave behind adrenaline fueled days, the excitement of the chase. The war..."

John tried to shut out his thoughts, the doubt that was creeping in. Mary had said that was all behind her. He wanted to believe her. But Mycroft was right, it is hard to walk away from that kind of life. What did he really know about Mary?

"So where do we start?" John sighed resignedly, as he stared at the coffee table.

Sherlock leaned back in his chair and said, "The broadcast. Someone wants us to think Moriarty is still alive, out there ready to reek havoc. Someone wants my attention."

Sherlock stood as he continued, "This afternoon, we'll meet with the best hacker I know. Find out how they were able to hack the system to broadcast that message."

Mycroft stood as well, punching in a text into his phone, "I have some arrangements to make and I am sure you both have some things to sort out. Anthea will return in 2 hours to collect you."

John didn't look at Mycroft as he left, just kept his gaze on the coffee table.

Sherlock looked down at his friend, slouched defeatedly on the sofa with a hollow gaze. Sherlock shifted his feet a bit before he walked over and sat next to John.

John turned his head slightly to acknowledge Sherlock as he sat, but he remained silent.

Sherlock wasn't certain how to make this right again. How to fix things for John. He leaned forward cautiously to look John in the eye.

"John, I'm-I'm sorry about this. I truly am. I wish - "

John's twittering laugh filled the air, "You're sorry? You're sorry...Sherlock, if anyone should be sorry, it's me. You killed Magnusson to protect me and Mary. She's my wife. I should have been the one to protect us, not you."

"John, I made a vow and I meant it. There's nothing I wouldn't do to protect you," Sherlock said very seriously.

John gave Sherlock a small smile and said "I know, you git. I just wish you didn't throw your whole life away in the process."

Sherlock just hummed in response and they sat in companionable silence for a moment. Sherlock considered a few options in his mind and as he settled on a decision, he turned to John.

"If you are going to be spending a considerable amount of time with me on this case then we should have Mary move here to Baker St, keep her close by," Sherlock said softly, trying not to scare John off from the idea.

John thought for a moment and then asked, "Why not you come to my house? It's a lot bigger."

Sherlock just shook his head and said, "I can't think anywhere else."

"It'll be too cramped here with three adults and a baby very soon," John said as he looked at Sherlock.

Sherlock nodded and remarked, "We'll rent 221C."

John paused to consider and then agreed, "Alright, alright. Anything to help keep her and the baby safe."

Sherlock stared at John with a blank expression.

"That's why you want her here, right? To keep he safe?" John asked.

Sherlock steepled his hands under his chin and said, "Yes, that...and to keep an eye on her."

**Author's Note:**

> If part of this chapter seems familiar to anyone, I had taken part of it from an old, discarded story of mine.


End file.
